diff --git a/src/resources/extensions/gsd/preferences.ts b/src/resources/extensions/gsd/preferences.ts
index a2c86fdbd..77d658fdd 100644
--- a/src/resources/extensions/gsd/preferences.ts
+++ b/src/resources/extensions/gsd/preferences.ts
@@ -389,6 +389,9 @@ function mergePreferences(base: GSDPreferences, override: GSDPreferences): GSDPr
     github: (base.github || override.github)
       ? { ...(base.github ?? {}), ...(override.github ?? {}) } as import("../github-sync/types.js").GitHubSyncConfig
       : undefined,
+    experimental: (base.experimental || override.experimental)
+      ? { ...(base.experimental ?? {}), ...(override.experimental ?? {}) }
+      : undefined,
     service_tier: override.service_tier ?? base.service_tier,
     forensics_dedup: override.forensics_dedup ?? base.forensics_dedup,
     show_token_cost: override.show_token_cost ?? base.show_token_cost,
diff --git a/src/resources/extensions/gsd/tests/preferences.test.ts b/src/resources/extensions/gsd/tests/preferences.test.ts
index 7e5f4177e..fa08a857e 100644
--- a/src/resources/extensions/gsd/tests/preferences.test.ts
+++ b/src/resources/extensions/gsd/tests/preferences.test.ts
@@ -10,10 +10,14 @@
 
 import test from "node:test";
 import assert from "node:assert/strict";
+import { mkdtempSync, mkdirSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
 import {
   validatePreferences,
   applyModeDefaults,
   getIsolationMode,
+  loadEffectiveGSDPreferences,
   parsePreferencesMarkdown,
   _resetParseWarningFlag,
 } from "../preferences.ts";
@@ -501,6 +505,55 @@ test("experimental.rtk parses correctly from preferences markdown", () => {
   assert.equal(prefs!.experimental?.rtk, true);
 });
 
+test("loadEffectiveGSDPreferences preserves experimental prefs across global+project merge", () => {
+  const originalCwd = process.cwd();
+  const originalGsdHome = process.env.GSD_HOME;
+  const tempProject = mkdtempSync(join(tmpdir(), "gsd-prefs-project-"));
+  const tempGsdHome = mkdtempSync(join(tmpdir(), "gsd-prefs-home-"));
+
+  try {
+    mkdirSync(join(tempProject, ".gsd"), { recursive: true });
+
+    writeFileSync(
+      join(tempGsdHome, "preferences.md"),
+      [
+        "---",
+        "version: 1",
+        "experimental:",
+        "  rtk: true",
+        "---",
+      ].join("\n"),
+      "utf-8",
+    );
+
+    writeFileSync(
+      join(tempProject, ".gsd", "PREFERENCES.md"),
+      [
+        "---",
+        "version: 1",
+        "git:",
+        "  isolation: none",
+        "---",
+      ].join("\n"),
+      "utf-8",
+    );
+
+    process.env.GSD_HOME = tempGsdHome;
+    process.chdir(tempProject);
+
+    const loaded = loadEffectiveGSDPreferences();
+    assert.notEqual(loaded, null);
+    assert.equal(loaded!.preferences.experimental?.rtk, true);
+    assert.equal(loaded!.preferences.git?.isolation, "none");
+  } finally {
+    process.chdir(originalCwd);
+    if (originalGsdHome === undefined) delete process.env.GSD_HOME;
+    else process.env.GSD_HOME = originalGsdHome;
+    rmSync(tempProject, { recursive: true, force: true });
+    rmSync(tempGsdHome, { recursive: true, force: true });
+  }
+});
+
 test("experimental.rtk defaults to off in new project preferences", () => {
   // No experimental key → feature is disabled
   const content = "---\nversion: 1\n---\n";